Iter-4360dd15-0145-transcript
第 145 轮执行轨迹
→ call search_memory({"limit":10,"query":"4360dd15 NEXT_FOCUS erratum alignment tool insertion replacement stress test"}) → call list_recent({"n":8})
→ call list_by_tag({"limit":10,"tag":"4360dd15"})
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0060-transcript", "tags": "iteration transcript", "modified": "20260424200117000", "preview": "!! 第 60 轮执行轨迹
→"}, {"title": "Iter-4360dd15-0094-transcript", "tags": "iteration transcript", "modified": "20260424210844000", "preview": "!! 第 94 轮执行轨迹 → call search_m"}, {"title": "Iter-4360dd15-0090-transcript", "tags": "iteration transcript", "modified": "20260424210019000", "preview": "!! 第 90 轮执行轨迹 【tool:list_recent】
{"ok": true, "items": [{"title": "Iter-4360dd15-0144-reflection", "modified": "20260424224634000", "tags": "iteration reflection"}, {"title": "NEXT_FOCUS", "modified": "20260424224634000", "tags": "pinned focus"}, {"title": "先做原句对齐再判定修正类型", "modified": "20260424224634000", "tags": "lesson erratum alignment verification"}, {"title": "Iter-4360dd15-0144-transcript", "modified": "20260424224629000", "tags": "iteration transcript"}, {"title": "Iter-4360dd15-0144-fact-BOLERO-2-erratum-word-alignment-context", "modified": "20260424224623000", "tags": "4360dd15 fact erratum verification method"}, {"title": "Iter-4360dd15-0143-reflection", "modified": "20260424224537000", "tags": "iteration reflection"}, {"title": "先锁定原句再做最小差分", "modified": "20260424224537000", "tags": "lesson erratum verbatim diff"}, {"title": "Iter-4360dd15-0143-transcript", "modified": "20260424224532000", "tags": "iteration transcript"}]}
【tool:list_by_tag】
{"ok": true, "items": [{"title": "Iter-4360dd15-0144-fact-BOLERO-2-erratum-word-alignment-context", "modified": "20260424224623000"}, {"title": "Iter-4360dd15-0143-fact-BOLERO-2-erratum-vertical-verbatim-pair", "modified": "20260424224527000"}, {"title": "Iter-4360dd15-0142-fact-BOLERO-2-erratum-redline-pair", "modified": "20260424224428000"}, {"title": "Iter-4360dd15-0138-fact-BOLERO-2-erratum-verbatim-pair", "modified": "20260424223553000"}, {"title": "BOLERO-2 PMC abstract erratum verbatim closed chain", "modified": "20260424222938000"}, {"title": "BOLERO-2 erratum abstract verbatim chain", "modified": "20260424222829000"}, {"title": "BOLERO-2 erratum: full corrected abstract sentence", "modified": "20260424222041000"}, {"title": "BOLERO-2 erratum: abstract correction scope corroborated from source text", "modified": "20260424221844000"}, {"title": "BOLERO-2 erratum: exact deleted abstract span", "modified": "20260424221738000"}, {"title": "BOLERO-2 PMID 22149876 vs PMC4713958: verbatim abstract diff", "modified": "20260424221644000"}]}
→ call read_note({"title":"NEXT_FOCUS"})
→ call list_tools({})
→ call search_memory({"limit":10,"query":"4360dd15 insertion replacement erratum PMC abstract correction alignment test"})
【tool:read_note】
{"ok": true, "title": "NEXT_FOCUS", "tags": "pinned focus", "text": "!! 下轮焦点（来自 mission 4360dd15 · Iter-0144）\n\n把词级对齐封装成可复用工具，并用一篇插入或替换型勘误做压力测试，验证不会把不同修正误判为纯删除。"}
【tool:list_tools】
{"ok": true, "tools": [{"name": "search_memory", "description": "在 TiddlyWiki 长期记忆中按关键字搜索（支持中文空格分隔），返回标题、标签、预览。每轮迭代开始前应先调用以回忆。", "custom": false}, {"name": "read_note", "description": "读取某一条 tiddler 的完整正文。", "custom": false}, {"name": "write_note", "description": "向 TiddlyWiki 写入（或覆盖）一条 tiddler。这是 Sisyphus 的长期记忆入口——每轮至少写一条。建议标签：knowledge, experiment, reflection, plan, idea, fact, question, lesson。TiddlyWiki 标记：!! 小标题，''粗体''，斜体，其它tiddler。", "custom": false}, {"name": "list_recent", "description": "列出最近修改过的 tiddler。", "custom": false}, {"name": "list_by_tag", "description": "按标签列出相关 tiddler。", "custom": false}, {"name": "run_python", "description": "在 workspace/ 下以子进程执行一段 Python 代码，返回 stdout/stderr。用于计算、模拟、验证假设、抓取公开数据（禁止任何破坏性操作）。", "custom": false}, {"name": "read_file", "description": "读取 workspace/ 下的某个文件。", "custom": false}, {"name": "write_file", "description": "向 workspace/ 下写入文件（默认覆盖，append=true 时追加）。", "custom": false}, {"name": "list_files", "description": "列出 workspace/ 下的文件。", "custom": false}, {"name": "web_fetch", "description": "抓取任意公开 URL（GET），返回剥离 HTML 后的纯文本。适合读论文摘要、文档、博客、百科。", "custom": false}, {"name": "web_search", "description": "用 DuckDuckGo 搜索互联网，返回 title/url/snippet 列表。找入口、找链接、调研时用。", "custom": false}, {"name": "wiki_search", "description": "维基百科搜索：返回若干条目的摘要和 URL。lang 默认 en，可传 zh 等。", "custom": false}, {"name": "arxiv_search", "description": "arXiv 论文检索：标题/作者/摘要/链接。理论、数学、物理、CS、bio 类前沿论文的主入口。", "custom": false}, {"name": "pubmed_search", "descriptio
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0131-transcript", "tags": "iteration transcript", "modified": "20260424222046000", "preview": "!! 第 131 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4713958 PMID 22149876 erratum abstract\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 PMID 22149876 PMC4713958 erratum abstract original corrected sentence\"}) → call list_recent({\"n\":8}) → call list_by_tag({\"limit\":10,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第"}, {"title": "Iter-4360dd15-0133-transcript", "tags": "iteration transcript", "modified": "20260424222632000", "preview": "!! 第 133 轮执行轨迹 → call pubmed_search({"limit":10,"query":"erratum abstract corrected sentence insertion replacement PMC"})
→ call web_search({"limit":10,"query":"site:pmc.ncbi.nlm.nih.gov erratum abstract corrected sentence insertion replacement PMC"})
【tool:pubmed_search】
{"ok": true, "query": "erratum abstract corrected sentence insertion replacement PMC", "results": []}
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov erratum abstract corrected sentence insertion replacement PMC", "results": [{"title": "Addressing Errors in Scientific Publishing: The Role of Errata - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11665756/", "snippet": "By publishing an erratum , publishers can ensure scientific accuracy and maintain ethical standards. This practice has several beneficial impacts: 1. Enhancing Trust and Transparency Trust is the cornerstone of scientific research. When journals openly admit and correct errors, it fosters trust among researchers, clinicians, and the public."}, {"title": "When things go wrong: correcting the scientific record - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC4609179/", "snippet": "A reliable scientific literature is crucial for an efficient research process. Peer review remains a highly successful quality assurance mechanism, but it does not always prevent data and image aberrations and the publication of flawed data. ..."}, {"title": "From honest mistakes to fake news - approaches to correcting the ...", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC7118961/", "snippet": "In the case of honest mistakes the principal aim should be to correct the work without harming the authors' reputation. Authors themselves have the opportunity of correcting, partially retracting or withdrawing their work with a detailed explanation regarding the reasons."}, {"title": "Why Correcting the Literature wit
→ call web_search({"limit":10,"query":"site:pmc.ncbi.nlm.nih.gov PMC erratum corrected abstract sentence inserted replaced"})
→ call pubmed_search({"limit":20,"query":"(erratum OR correction) abstract corrected sentence PMC"})
→ call search_memory({"limit":10,"query":"4360dd15 corrected abstract insertion replacement erratum candidate"})
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov PMC erratum corrected abstract sentence inserted replaced", "results": [{"title": "PMC Home", "url": "https://pmc.ncbi.nlm.nih.gov/", "snippet": "PMC is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM)."}, {"title": "PMC User Guide - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/about/userguide/", "snippet": "PMC User Guide PubMed Central® ( PMC ) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM). This guide is meant to help you use PMC to find and read articles of interest to you. Answers to many common questions about PMC are available in the PMC FAQ."}, {"title": "Addressing Errors in Scientific Publishing: The Role of Errata - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11665756/", "snippet": "By publishing an erratum , publishers can ensure scientific accuracy and maintain ethical standards. This practice has several beneficial impacts: 1. Enhancing Trust and Transparency Trust is the cornerstone of scientific research. When journals openly admit and correct errors, it fosters trust among researchers, clinicians, and the public."}, {"title": "For Authors - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/about/submission-methods/", "snippet": "For Authors PubMed Central ( PMC ) is a free full-
【tool:pubmed_search】
{"ok": true, "query": "(erratum OR correction) abstract corrected sentence PMC", "results": [{"pmid": "39363538", "title": "Addressing Drug-Drug Interaction Knowledge Gaps at the Time of Approval: An Analysis of FDA Postmarketing Requirements and Commitments from 2009 to 2023.", "source": "J Clin Pharmacol", "pubdate": "2025 Mar", "authors": ["Ridge S", "Yang X", "Madabushi R", "Ramamoorthy A"], "url": "https://pubmed.ncbi.nlm.nih.gov/39363538/"}]}
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0060-transcript", "tags": "iteration transcript", "modified": "20260424200117000", "preview": "!! 第 60 轮执行轨迹
→ call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS 剩余 10 条候选 PMID 研究类型 保留 排除 理由 extension follow-up secondary analysis\"}) → call list_recent({\"n\":10}) → call list_tools({}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0059-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424195947000\", \"preview\": \"!! 第 59 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 NEXT_FOCUS PMC4713958 PMID 22149876 erratum abstract\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0060-transcript\", \"tags\": \"iteration transcript\", \"modified\": \"20260424200117000\", \"preview\": \"!! 第 60 轮执行轨迹 → call search_memory({\"limit\":10,\"query\":\"4360dd15 38310895 NEXT_FOCUS 原始人类试验 PMID 主要终点\"}) → call list_recent({\"n\":10}) → call list_by_tag({\"limit\":10,\"tag\":\"4360dd15\"}) 【tool:search_memory】 {\"ok\": tru → call define_tool({"name":"erratum_text_edit_classifier","description":"Classify the minimal edit between an original sentence and corrected sentence as deletion/insertion/replacement using a token-level diff; returns spans and edit type for reusable erratum verification.","code":"import difflib\nimport re\nfrom typing import List, Tuple\n\ndef _tok(text: str) -> List[str]:\n # whitespace tokenization with punct)
→ call web_search({"limit":10,"query":"site:pmc.ncbi.nlm.nih.gov erratum abstract replacement corrected sentence PMC \"corrected abstract\""})
→ call search_memory({"limit":10,"query":"4360dd15 candidate insertion replacement erratum abstract PMC correction"})
【tool:define_tool】
{"ok": false, "error": "参数错误: tool_define_tool() missing 1 required positional argument: 'parameters'"}
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov erratum abstract replacement corrected sentence PMC \"corrected abstract\"", "results": []}
【tool:search_memory】
{"ok": true, "results": [{"title": "Iter-4360dd15-0131-transcript", "tags": "iteration transcript", "modified": "20260424222046000", "preview": "!! 第 131 轮执行轨迹
→ call search_memory({\\\"limit\\\":10,\\\"query\\\":\\\"4360dd15 NEXT_FOCUS 剩余 10 条候选 PMID 研"}, {"title": "Iter-4360dd15-0127-transcript", "tags": "iteration transcript", "modified": "20260424221544000", "preview": "!! 第 127 轮执行轨迹 → call search_memory({\"limit\":8,\"query\":\"4360dd15 erratum abstract PMID PMCID DOI BOLERO-2 original erratum verbatim\"}) 【tool:search_memory】 {\"ok\": true, \"results\": [{\"title\": \"Iter-4360dd15-0131-transcr → call web_search({"limit":10,"query":"site:pmc.ncbi.nlm.nih.gov \"Erratum\" abstract corrected sentence inserted replaced \"PMC\""})
→ call web_search({"limit":10,"query":"site:pmc.ncbi.nlm.nih.gov \"correction\" \"abstract\" \"erratum\" \"should read\" PMC"})
→ call pubmed_search({"limit":20,"query":"erratum abstract should read PMC should read abstract"})
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov \"Erratum\" abstract corrected sentence inserted replaced \"PMC\"", "results": []}
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov \"correction\" \"abstract\" \"erratum\" \"should read\" PMC", "results": []}
【tool:pubmed_search】
{"ok": true, "query": "erratum abstract should read PMC should read abstract", "results": []}
→ call web_search({"limit":10,"query":"PMC erratum abstract replace words corrected sentence \"should be\""})
→ call web_search({"limit":10,"query":"PMC erratum abstract insert words corrected sentence \"read as\""})
→ call web_search({"limit":10,"query":"PMC correction abstract sentence replacement erratum exact wording"})
【tool:web_search】
{"ok": true, "query": "PMC erratum abstract replace words corrected sentence \"should be\"", "results": []}
【tool:web_search】
{"ok": true, "query": "PMC erratum abstract insert words corrected sentence \"read as\"", "results": []}
【tool:web_search】
{"ok": true, "query": "PMC correction abstract sentence replacement erratum exact wording", "results": [{"title": "PDF Guide for the Publication of Erratum", "url": "https://www.scielo.org/documents/70/guia_errata_en.pdf", "snippet": "An Erratum is a correction of errors identified in documents already published. Publishing an erratum is necessary when the author of the document or the editor of the journal identify one or more errors in the published document."}, {"title": "Addressing Errors in Scientific Publishing: The Role of Errata - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC11665756/", "snippet": "By publishing an erratum , publishers can ensure scientific accuracy and maintain ethical standards. This practice has several beneficial impacts: 1. Enhancing Trust and Transparency Trust is the cornerstone of scientific research. When journals openly admit and correct errors, it fosters trust among researchers, clinicians, and the public."}, {"title": "PMC Corrections documents Documentation", "url": "https://pmc-3.readthedocs.io/_/downloads/en/latest/pdf/", "snippet": "The purpose of this document is to provide simple, but detailed guide to the realm of PMC corrections . We suggest starting with \"Getting started\" page and working your way through the rest of the pages step by step. Happy hunting!"}, {"title": "Retraction Resources", "url": "https://www.councilscienceeditors.org/retraction-resources", "snippet": "PURPOSE This compilation of primary guidance do
→ call web_search({"limit":20,"query":"site:pmc.ncbi.nlm.nih.gov PMC erratum \"should read\" abstract \"corrected to\""})
→ call web_search({"limit":20,"query":"site:pmc.ncbi.nlm.nih.gov PMC corrigendum abstract \"should read\""})
→ call web_search({"limit":20,"query":"site:pmc.ncbi.nlm.nih.gov PMC correction abstract replacement sentence"})
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov PMC erratum \"should read\" abstract \"corrected to\"", "results": []}
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov PMC corrigendum abstract \"should read\"", "results": [{"title": "Perirenal fat stranding is not a powerful diagnostic tool for acute ...", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5823068/", "snippet": "Page 137, Abstract , Results, the text \"The frequency of PFS was 72% in the pyelonephritis group vs 39% in the control group\" should read \"The frequency of PFS was 72% in the pyelonephritis group vs 29% in the control group\". Page 140, Table 1, Control (PRB) column, last row, the data \"93 (39%)\" should read \"93 (29%)\"."}, {"title": "Corrigendum to \"Reducing conflict and containment rates on acute ...", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5611482/", "snippet": "The reduction in the rate of conflict should read 15% (95% CI 5.7-23.7%) and containment 23.2% (95% CI 9.9-35.5%) in the abstract and Section 2.1. Table 1 row 8 for PCC containment, risk of events - n / N should read 0.58 (938/1607) experimental, and 0.50 (802/1609) control. In Table 2, the confidence intervals for physical health should read −3.702 to −0.003, and the corresponding ..."}, {"title": "Art of reading a journal article: Methodically and effectively - PMC", "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC3687192/", "snippet": "ABSTRACT Abstract helps us determine whether we should read the entire article or not. In fact, most journals provide abstract free of cost online allowing us to decide whether we need to purchase the entir
【tool:web_search】
{"ok": true, "query": "site:pmc.ncbi.nlm.nih.gov PMC correction abstract replacement sentence", "results": []}
→ call web_fetch({"max_chars":8000,"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5823068/"})
→ call web_fetch({"max_chars":8000,"url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC5611482/"})
【tool:web_fetch】
{"ok": true, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5823068/", "status": 200, "content_type": "text/html; charset=utf-8", "text": "Perirenal fat stranding is not a powerful diagnostic tool for acute pyelonephritis [Corrigendum] - PMC Skip to main content An official website of the United States government Here's how you know Here's how you know Official websites use .gov A .gov website belongs to an official government organization in the United States. Secure .gov websites use HTTPS A lock ( Lock Locked padlock icon ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites. Search Log in Dashboard Publications Account settings Log out Search… Search NCBI Primary site navigation Search Logged in as: Dashboard Publications Account settings Log in Search PMC Full-Text Archive Search in PMC Journal List User Guide PERMALINK Copy As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health. Learn more: PMC Disclaimer | PMC Copyright Notice Int J Gen Med . 2018 Feb 19;11:79. doi: 10.2147/IJGM.S164399 Search in PMC Search in PubMed View in NLM Catalog Add to search Perirenal fat stranding is not a powerful diagnostic tool for acute pyelonephritis [Corrigendum] Article notes Copyright and License information Collection date 2018. © 2018 Fukami et al. This work is published
【tool:web_fetch】
{"ok": true, "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC5611482/", "status": 200, "content_type": "text/html; charset=utf-8", "text": "Corrigendum to “Reducing conflict and containment rates on acute psychiatric wards: The Safewards cluster randomised controlled trial” [Int. J. Nurs. Stud. 52 (September (9)) (2015) 1412–1422] - PMC Skip to main content An official website of the United States government Here's how you know Here's how you know Official websites use .gov A .gov website belongs to an official government organization in the United States. Secure .gov websites use HTTPS A lock ( Lock Locked padlock icon ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites. Search Log in Dashboard Publications Account settings Log out Search… Search NCBI Primary site navigation Search Logged in as: Dashboard Publications Account settings Log in Search PMC Full-Text Archive Search in PMC Journal List User Guide PERMALINK Copy As a library, NLM provides access to scientific literature. Inclusion in an NLM database does not imply endorsement of, or agreement with, the contents by NLM or the National Institutes of Health. Learn more: PMC Disclaimer | PMC Copyright Notice Int J Nurs Stud . 2016 Jun;58:102. doi: 10.1016/j.ijnurstu.2015.12.006 Search in PMC Search in PubMed View in NLM Catalog Add to search Corrigendum to “Reducing conflict and containment rates on acute psychiatric wards: The Safewards cluste
→ call define_tool({"name":"erratum_text_edit_classifier","description":"Classify the minimal edit between an original sentence and corrected sentence as deletion/insertion/replacement using a token-level diff; re